[2024-01-24 13:17:45,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:45,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:45,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference
[2024-01-24 13:17:47,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:47,025] [INFO] Task started: Prodigal
[2024-01-24 13:17:47,025] [INFO] Running command: gunzip -c /var/lib/cwl/stgee97588d-0f6f-437c-8264-2437193d1f3c/GCF_000744735.1_ASM74473v1_genomic.fna.gz | prodigal -d GCF_000744735.1_ASM74473v1_genomic.fna/cds.fna -a GCF_000744735.1_ASM74473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:54,415] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:54,416] [INFO] Task started: HMMsearch
[2024-01-24 13:17:54,416] [INFO] Running command: hmmsearch --tblout GCF_000744735.1_ASM74473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference/reference_markers.hmm GCF_000744735.1_ASM74473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:54,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:54,715] [INFO] Found 6/6 markers.
[2024-01-24 13:17:54,742] [INFO] Query marker FASTA was written to GCF_000744735.1_ASM74473v1_genomic.fna/markers.fasta
[2024-01-24 13:17:54,742] [INFO] Task started: Blastn
[2024-01-24 13:17:54,742] [INFO] Running command: blastn -query GCF_000744735.1_ASM74473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference/reference_markers.fasta -out GCF_000744735.1_ASM74473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:55,451] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:55,455] [INFO] Selected 29 target genomes.
[2024-01-24 13:17:55,456] [INFO] Target genome list was writen to GCF_000744735.1_ASM74473v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:55,471] [INFO] Task started: fastANI
[2024-01-24 13:17:55,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgee97588d-0f6f-437c-8264-2437193d1f3c/GCF_000744735.1_ASM74473v1_genomic.fna.gz --refList GCF_000744735.1_ASM74473v1_genomic.fna/target_genomes.txt --output GCF_000744735.1_ASM74473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:19,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:19,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:19,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:19,115] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:19,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:19,115] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	100.0	824	824	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:18:19,117] [INFO] DFAST Taxonomy check result was written to GCF_000744735.1_ASM74473v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:19,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:19,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:19,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference/checkm_data
[2024-01-24 13:18:19,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:19,148] [INFO] Task started: CheckM
[2024-01-24 13:18:19,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000744735.1_ASM74473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000744735.1_ASM74473v1_genomic.fna/checkm_input GCF_000744735.1_ASM74473v1_genomic.fna/checkm_result
[2024-01-24 13:18:48,298] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:48,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,320] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:48,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:48,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000744735.1_ASM74473v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:48,321] [INFO] Task started: Blastn
[2024-01-24 13:18:48,321] [INFO] Running command: blastn -query GCF_000744735.1_ASM74473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd6f70ca-8dbd-43de-a4e4-303a52d6e019/dqc_reference/reference_markers_gtdb.fasta -out GCF_000744735.1_ASM74473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:49,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:49,466] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:49,466] [INFO] Target genome list was writen to GCF_000744735.1_ASM74473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:49,492] [INFO] Task started: fastANI
[2024-01-24 13:18:49,493] [INFO] Running command: fastANI --query /var/lib/cwl/stgee97588d-0f6f-437c-8264-2437193d1f3c/GCF_000744735.1_ASM74473v1_genomic.fna.gz --refList GCF_000744735.1_ASM74473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000744735.1_ASM74473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:55,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,295] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:55,296] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	100.0	824	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	conclusive
GCA_002707685.1	s__Porticoccus sp002707685	94.5946	742	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002341315.1	s__Porticoccus sp002341315	94.2671	711	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733125.1	s__Porticoccus sp002733125	94.0646	624	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003235325.1	s__SZUA-272 sp003235325	76.5149	57	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__SZUA-272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066715.1	s__Porticoccus sp018066715	76.5144	89	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.88	99.88	0.93	0.93	2	-
GCA_006227015.1	s__Porticoccus sp006227015	76.4625	84	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011049795.1	s__Porticoccus sp011049795	76.0188	65	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,297] [INFO] GTDB search result was written to GCF_000744735.1_ASM74473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:55,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:55,300] [INFO] DFAST_QC result json was written to GCF_000744735.1_ASM74473v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:55,300] [INFO] DFAST_QC completed!
[2024-01-24 13:18:55,301] [INFO] Total running time: 0h1m10s